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- PDB-8c4l: Ferric-siderophore reduction in Shewanella biscestrii: Structural... -

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Basic information

Entry
Database: PDB / ID: 8c4l
TitleFerric-siderophore reduction in Shewanella biscestrii: Structural and functional characterization of SbiSIP reveals unforeseen specificity
ComponentsVibriobactin utilization protein ViuB
KeywordsMETAL BINDING PROTEIN / Siderophore binding protein / Iron reduction / metal transport
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Vibriobactin utilization protein ViuB
Similarity search - Component
Biological speciesShewanella bicestrii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsTrindade, I.B. / Matias, P. / Moe, E. / Louro, R.O.
Funding support Portugal, European Union, 6items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPD/BD/135187/2017 Portugal
Fundacao para a Ciencia e a Tecnologiat PTDC/BIA-BQM/30176/2017 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04612/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04612/2020 Portugal
European Union (EU)Project 810856European Union
Fundacao para a Ciencia e a TecnologiaAAC 01/SAICT/2016 Portugal
CitationJournal: To be published
Title: Ferric-siderophore reduction in Shewanella bicestrii: Structural and functional characterization of SbSIP reveals an overlooked specificity of siderophore interacting proteins
Authors: Trindade, I.B. / Fonseca, B.M. / Catarino, T. / Matias, P. / Moe, E. / Louro, R.O.
History
DepositionJan 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vibriobactin utilization protein ViuB
B: Vibriobactin utilization protein ViuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6474
Polymers56,0762
Non-polymers1,5712
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-28 kcal/mol
Surface area22540 Å2
Unit cell
Length a, b, c (Å)82.441, 82.441, 250.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

21A-777-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 246 or resid 500))
d_2ens_1(chain "B" and (resid 6 through 246 or resid 500))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLUA3 - 243
d_12ens_1FADFADB
d_21ens_1PROGLUC1 - 241
d_22ens_1FADFADD

NCS oper: (Code: givenMatrix: (-0.651442399611, -0.749997619649, 0.114570373612), (0.732852093426, -0.661113770254, -0.160799228676), (0.196343090406, -0.0207882972388, 0.980314866534)Vector: 74. ...NCS oper: (Code: given
Matrix: (-0.651442399611, -0.749997619649, 0.114570373612), (0.732852093426, -0.661113770254, -0.160799228676), (0.196343090406, -0.0207882972388, 0.980314866534)
Vector: 74.9222054144, -25.1356024154, 23.5481810389)

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Components

#1: Protein Vibriobactin utilization protein ViuB


Mass: 28037.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella bicestrii (bacteria) / Gene: viuB, NCTC12093_01939 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A448CKI9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 1.8 M Ammonium sulfate with 0.01 M Cobalt(II) chloride hexahydrate and 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.86→62.71 Å / Num. obs: 49068 / % possible obs: 93.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 30.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 19.3
Reflection shellResolution: 1.86→2.03 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2453 / CC1/2: 0.819 / Rpim(I) all: 0.333 / Rrim(I) all: 0.82 / % possible all: 15

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→62.71 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1995 2412 4.92 %
Rwork0.1678 46650 -
obs0.1694 49062 66.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.78 Å2
Refinement stepCycle: LAST / Resolution: 1.86→62.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 106 323 4255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01224031
X-RAY DIFFRACTIONf_angle_d1.14525497
X-RAY DIFFRACTIONf_chiral_restr0.063602
X-RAY DIFFRACTIONf_plane_restr0.0117699
X-RAY DIFFRACTIONf_dihedral_angle_d14.63591477
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.816756801419 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90.492580.2528155X-RAY DIFFRACTION3.88
1.9-1.940.2236240.2281468X-RAY DIFFRACTION11.62
1.94-1.990.2397500.2336777X-RAY DIFFRACTION19.65
1.99-2.040.2703610.19551086X-RAY DIFFRACTION26.93
2.04-2.090.2493640.20331329X-RAY DIFFRACTION32.78
2.09-2.150.2328900.20511658X-RAY DIFFRACTION41.21
2.15-2.220.22861070.18642077X-RAY DIFFRACTION51.15
2.22-2.30.22251310.20342571X-RAY DIFFRACTION63.53
2.3-2.40.2341560.20313404X-RAY DIFFRACTION83.27
2.4-2.50.23671860.19893978X-RAY DIFFRACTION97.27
2.5-2.640.23352190.19124050X-RAY DIFFRACTION99.23
2.64-2.80.23622080.18844066X-RAY DIFFRACTION99.46
2.8-3.020.22382100.18454099X-RAY DIFFRACTION99.63
3.02-3.320.21722380.17354102X-RAY DIFFRACTION99.5
3.32-3.80.17092420.14044121X-RAY DIFFRACTION99.73
3.8-4.790.15152190.12534222X-RAY DIFFRACTION99.87
4.79-62.710.19761990.1794487X-RAY DIFFRACTION99.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.782081747039-0.817836696797-0.07228224836842.830754528-0.3729318736853.76426758408-0.0878555318949-0.174581446024-0.106666009610.483952868320.1479074406670.1306952715270.132454372723-0.158474123354-0.05989094624030.296175683892-0.000739898655126-0.00477928312890.1498300079550.0172161789790.20986932492733.73559794361.9401544099714.1309540781
21.088035289470.8035574081760.2661029932894.00766832079-0.0818821134525.273490847060.344295415436-0.216020074031-0.4118891653910.260166716013-0.08324340757320.5713683438930.158471669176-1.05016919974-0.2800519901360.324718518299-0.1309618488180.07543275214390.2896290455570.1353495708510.2785946571723.4393493463-3.6419561802914.8473072049
33.02277371781-0.530606844743-0.1006959938392.009560371220.01494637983943.56902197467-0.0419200477088-0.1282423026750.04131579249780.3992076076570.08641203994360.164040890043-0.109502894082-0.209049735542-0.03881189785950.2713850181620.003012318690730.02819942289540.1356362850920.01050813410010.18679378816729.94875273083.2679231304813.0020060384
40.964748549076-0.448818409547-0.2866589573970.9540007475632.133476315175.57916643953-0.1280132564480.0286231931156-0.556846105909-0.318968842519-0.05072852908460.1938887855830.79138102734-0.5852461176410.3563143983310.618598940653-0.1916368390160.0414106804640.161319480643-0.05107736824560.37827839724828.6700981857-11.2260918469-4.1350107244
52.452005584090.342118322149-0.5363125004422.535760529980.1397683997615.23033844368-0.006296023009710.297139735450.0359393004678-0.07345519507820.04994313892340.03768610105150.117539896108-0.142338926434-0.01081060994950.0998417359321-0.00826746806098-0.01713321547530.152108763952-0.007366935921940.15874048213535.06611436853.0457949155-9.75464986046
60.3039126353270.483272732399-0.144505616491.46720661768-0.242727153284.253234584950.01985599090020.775282689449-0.100424476431-0.4895276790190.375551730781.064197442990.0958981959467-2.39461410440.910542967953-0.161127618818-0.21826478229-0.1761548588220.565450435742-0.03841004583630.18732609859122.1971799190.959926851032-10.3254593133
70.7152954656-0.8774528291680.483409591311.922919290841.817384661177.29598929408-0.136180097110.937336045214-0.67658653813-0.1441363901810.3005044359010.4431128920640.748796847048-1.113877401450.1577943998190.259868641172-0.08139003517860.0827724376291.00222598372-0.01432115641490.56824968323712.37995042541.92304383601-2.18111000927
82.64251301980.1162801241490.5635529442622.10248885020.3918749853913.997767057510.088702406434-0.09375104044280.111544790770.1449965511280.0910619783085-0.3141005074890.07714235990720.56438793221-0.1505647719520.1964844314750.047643532314-0.0008391009774160.23350834465-0.01143742406490.25118343689956.0465212502-1.2501128133343.3594439234
91.22594623635-1.190128227561.389694486986.92895943311-0.6845085494722.081714890540.02779937785420.136612804553-0.2044574095370.693876323419-0.3585385065850.1019426435650.4331609288530.03083763691450.1911698760070.3546278522460.1757246633340.02545639938770.312516251869-0.009722525553830.41981439214164.1310964596-16.573485620443.477897072
102.005459206010.1036962924010.4913714148011.243643864460.7504321784673.37981375152-0.05282506058880.162400219354-0.00315505542221-0.09725058982450.133727264138-0.1745589035540.03737257663250.6761553340920.02077387137740.2023313319610.02374924081540.0125588841890.169832777168-0.01201269147480.21716696914355.1814871417-2.1028031666533.0374062322
113.03715788835-0.1068414619080.1634154514511.96733141003-0.2890426790314.12839599529-0.07068555876480.674889793178-0.191586367485-0.4425269274440.113053190621-0.1473537902560.1687590479540.4649772509550.05328302478880.3024960261870.01327129477690.02757757809520.304417211176-0.05797667159460.17125407420249.7949940402-3.8878432834617.8143749237
122.57678905497-0.1888012436841.191145070253.70461547829-0.1756398310673.22725234321-0.131079236270.982946086154-0.376729463402-0.2940025718890.039615988852-0.9738239029770.571527686761.495450394540.5240201598490.3601106068430.1469792620050.1073001233130.575129479599-0.1850799296860.35929724309960.459608043-8.4042611186320.8910905733
131.002533670240.4028866167762.30631781143.30814232916-2.131203923078.39986660256-0.1019234953470.65316854309-0.6518570636010.03011478809160.22622260369-0.7470798955820.3606456279221.68065638181-0.05944017411670.6339928132920.3397655243850.08835917816880.861286266974-0.1924850576740.74752469964465.9018015073-16.428739782822.5758934972
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 27 )AA4 - 271 - 24
22chain 'A' and (resid 28 through 55 )AA28 - 5525 - 52
33chain 'A' and (resid 56 through 98 )AA56 - 9853 - 95
44chain 'A' and (resid 99 through 112 )AA99 - 11296 - 109
55chain 'A' and (resid 113 through 190 )AA113 - 190110 - 187
66chain 'A' and (resid 191 through 231 )AA191 - 231188 - 228
77chain 'A' and (resid 232 through 246 )AA232 - 246229 - 243
88chain 'B' and (resid 6 through 41 )BC6 - 411 - 36
99chain 'B' and (resid 42 through 55 )BC42 - 5537 - 50
1010chain 'B' and (resid 56 through 145 )BC56 - 14551 - 140
1111chain 'B' and (resid 146 through 213 )BC146 - 213141 - 208
1212chain 'B' and (resid 214 through 231 )BC214 - 231209 - 226
1313chain 'B' and (resid 232 through 248 )BC232 - 248227 - 243

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